1887

Abstract

species are vector-borne parasitic bacteria with unusual, highly fragmented genomes that include a linear chromosome and linear as well as circular plasmids that differ numerically between and within various species. Strain CA690, which was cultivated from a questing nymph in the San Francisco Bay area, CA, was determined to be genetically distinct from all other described species belonging to the complex. The genome, including plasmids, was assembled using a hybrid assembly of short Illumina reads and long reads obtained via Oxford Nanopore Technology. We found that strain CA690 has a main linear chromosome containing 902176 bp with a identity ≤91 % compared with other species chromosomes and five linear and two circular plasmids. A phylogeny based on 37 single-copy genes of the main linear chromosome and rooted with the relapsing fever species strain Ly revealed that strain CA690 had a sister-group relationship with, and occupied a basal position to, species occurring in North America. We propose to name this species sp. nov. The type strain, CA690, has been deposited in two national culture collections, DSMZ (=107169) and ATCC (=TSD-160)

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003833
2019-12-03
2024-11-13
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/2/849.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003833&mimeType=html&fmt=ahah

References

  1. Gern L, Humair P. Ecology of Borrelia burgdorferi sensu lato in Europe. In Gray JS, Kahl O, Lane RS, Stanek G. (editors) Lyme Borreliosis: Biology, Epidemiology and Control Wallingford: CABI Publishing; 2002 pp 149–174
    [Google Scholar]
  2. Kurtenbach K, Hanincová K, Tsao JI, Margos G, Fish D et al. Fundamental processes in the evolutionary ecology of Lyme borreliosis. Nat Rev Microbiol 2006; 4:660–669 [View Article]
    [Google Scholar]
  3. Piesman J, Schwan TG. Ecology of borreliae and their arthropod vectors. In Samuels DS, Radolf JD. (editors) Borrelia: Molecular Biology, Host Interaction and Pathogenesis Caister Academic Press; 2010 pp 251–278
    [Google Scholar]
  4. Kurtenbach K, Hoen AG, Bent SJ, Vollmer SA, Ogden NH et al. Population Biology of Lyme Borreliosis spirochetes. In Robinson DA, Falush D, Feil EJ. (editors) Bacterial Population Genetics in Infectious Disease John Wiley & Sons, Inc; 2010
    [Google Scholar]
  5. Tsao JI. Reviewing molecular adaptations of Lyme borreliosis spirochetes in the context of reproductive fitness in natural transmission cycles. Vet Res 2009; 40:36 [View Article]
    [Google Scholar]
  6. Casjens SR, Mongodin EF, Qiu WG, Luft BJ, Schutzer SE et al. Genome stability of Lyme disease spirochetes: comparative genomics of Borrelia burgdorferi plasmids. PLoS One 2012; 7:e33280 [View Article]
    [Google Scholar]
  7. Fraser CM, Casjens S, Huang WM, Sutton GG, Clayton R et al. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi . Nature 1997; 390:580–586 [View Article]
    [Google Scholar]
  8. Chaconas G, Kobryn K, Structure KK. Structure, function, and evolution of linear replicons in Borrelia . Annu Rev Microbiol 2010; 64:185–202 [View Article]
    [Google Scholar]
  9. Casjens SR, Gilcrease EB, Vujadinovic M, Mongodin EF, Luft BJ et al. Plasmid diversity and phylogenetic consistency in the Lyme disease agent Borrelia burgdorferi . BMC Genomics 2017; 18:165 [View Article]
    [Google Scholar]
  10. Becker NS, Margos G, Blum H, Krebs S, Graf A et al. Recurrent evolution of host and vector association in bacteria of the Borrelia burgdorferi sensu lato species complex. BMC Genomics 2016; 17:734 [View Article]
    [Google Scholar]
  11. Margos G, Fedorova N, Kleinjan JE, Hartberger C, Schwan TG et al. Borrelia lanei sp. nov. extends the diversity of Borrelia species in California. Int J Syst Evol Microbiol 2017; 67:3872–3876 [View Article]
    [Google Scholar]
  12. Pritt BS, Respicio-Kingry LB, Sloan LM, Schriefer ME, Replogle AJ et al. Borrelia mayonii sp. nov., a member of the Borrelia burgdorferi sensu lato complex, detected in patients and ticks in the upper midwestern United States. Int J Syst Evol Microbiol 2016; 66:4878–4880 [View Article]
    [Google Scholar]
  13. Fedorova N, Kleinjan JE, James D, Hui LT, Peeters H et al. Remarkable diversity of tick or mammalian-associated borreliae in the metropolitan San Francisco Bay area, California. Ticks Tick Borne Dis 2014; 5:951–961 [View Article]
    [Google Scholar]
  14. Margos G, Vollmer SA, Cornet M, Garnier M, Fingerle V et al. A new Borrelia species defined by multilocus sequence analysis of housekeeping genes. Appl Environ Microbiol 2009; 75:5410–5416 [View Article]
    [Google Scholar]
  15. Postic D, Garnier M, Baranton G. Multilocus sequence analysis of atypical Borrelia burgdorferi sensu lato isolates--description of Borrelia californiensis sp. nov., and genomospecies 1 and 2. Int J Med Microbiol 2007; 297:263–271 [View Article]
    [Google Scholar]
  16. Ruzic-Sabljic E, STRLE F, Arnez M, Lotric-Furlan S, Maraspin V et al. Genotypic and phenotypic characterisation of Borrelia burgdorferi sensu lato strains isolated from human blood. J Med Microbiol 2001; 50:896–901 [View Article]
    [Google Scholar]
  17. Preac-Mursic V, Wilske B, Schierz G. European Borrelia burgdorferi isolated from humans and ticks culture conditions and antibiotic susceptibility. Zentralbl Bakteriol Mikrobiol Hyg A 1986; 263:112–118 [View Article]
    [Google Scholar]
  18. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 2013; 20:714–737 [View Article]
    [Google Scholar]
  19. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article]
    [Google Scholar]
  20. Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R. Galaxy: a web-based genome analysis tool for experimentalists. In Ausubel FM. editor Current Protocols in Molecular Biology 19 2010 pp 11–21
    [Google Scholar]
  21. Antipov D, Korobeynikov A, McLean JS, Pevzner PA. hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics 2016; 32:1009–1015 [View Article]
    [Google Scholar]
  22. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article]
    [Google Scholar]
  23. Gish W, States DJ. Identification of protein coding regions by database similarity search. Nat Genet 1993; 3:266–272 [View Article]
    [Google Scholar]
  24. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article]
    [Google Scholar]
  25. Petkau A, Stuart-Edwards M, Stothard P, Van Domselaar G. Interactive microbial genome visualization with GView. Bioinformatics 2010; 26:3125–3126 [View Article]
    [Google Scholar]
  26. Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14:1394–1403 [View Article]
    [Google Scholar]
  27. Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. Blast ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011; 12:402 [View Article]
    [Google Scholar]
  28. Gillespie JJ, Wattam AR, Cammer SA, Gabbard JL, Shukla MP et al. PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun 2011; 79:4286–4298 [View Article]
    [Google Scholar]
  29. Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T et al. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 2014; 42:D581–D591 [View Article]
    [Google Scholar]
  30. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016; 4:e1900v1901
    [Google Scholar]
  31. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article]
    [Google Scholar]
  32. Edgar RC. Muscle: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004; 5:113 [View Article]
    [Google Scholar]
  33. Drummond AJ, Rambaut A. Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007; 7:214 [View Article]
    [Google Scholar]
  34. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. In Miura RM. editor Some Mathematical Questions in Biology: DNA Sequence Analysis American Mathematical Society; 1986 pp 57–86
    [Google Scholar]
  35. Stadler T. On incomplete sampling under birth–death models and connections to the sampling-based coalescent. J Theor Biol 2009; 261:58–66 [View Article]
    [Google Scholar]
  36. Sokal RR, Michener CD. A statistical Method for Evaluating Systematic Relationships University of Kansas; 1958
    [Google Scholar]
  37. Rambaut A, Suchard MA, Xie D, Drummond AJ. 2014; Tracer v1.6. http://beastbioedacuk/Tracer
  38. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article]
    [Google Scholar]
  39. Casjens S, Eggers CH, Schwartz I. Borrelia genomics: chromosome, plasmids, bacteriohpages and genetic variation. In Samuels DS, Radolf J. (editors) Borrelia - Molecular Biology, Host Interaction and Pathogenesis Caister Academic Press; 2010 pp 27–53
    [Google Scholar]
  40. Wywial E, Haven J, Casjens SR, Hernandez YA, Singh S et al. Fast, adaptive evolution at a bacterial host-resistance locus: the PFam54 gene array in Borrelia burgdorferi . Gene 2009; 445:26–37 [View Article]
    [Google Scholar]
  41. Eisen L, Eisen RJ, Lane RS. Geographical distribution patterns and habitat suitability models for presence of host-seeking ixodid ticks in dense woodlands of Mendocino County, California. J Med Entomol 2006; 43:415–427 [View Article]
    [Google Scholar]
  42. Brown R, Lane R. Lyme disease in California: a novel enzootic transmission cycle of Borrelia burgdorferi . Science 1992; 256:1439–1442 [View Article]
    [Google Scholar]
  43. Eisen L, Eisen RJ, Lane RS. The roles of birds, lizards, and rodents as hosts for the western black-legged tick Ixodes pacificus . J Vector Ecol 2004; 29:295–308
    [Google Scholar]
  44. Furman DP, Loomis EC. The ticks of California (Acari:Ixodida). Bul Calif Insect Survey 1984; 25:1–239
    [Google Scholar]
  45. Heylen D, Krawczyk A, Lopes de Carvalho I, Núncio MS, Sprong H et al. Bridging of cryptic Borrelia cycles in European songbirds. Environ Microbiol 2017; 19:1857–1867 [View Article]
    [Google Scholar]
  46. Heylen D, Tijsse E, Fonville M, Matthysen E, Sprong H. Transmission dynamics of Borrelia burgdorferi s.l. in a bird tick community. Environ Microbiol 2013; 15:663–673 [View Article]
    [Google Scholar]
  47. Norte AC, Ramos JA, Gern L, Núncio MS, Lopes de Carvalho I. Birds as reservoirs for Borrelia burgdorferi s.l. in Western Europe: circulation of B. turdi and other genospecies in bird-tick cycles in Portugal. Environ Microbiol 2013; 15:386–397 [View Article]
    [Google Scholar]
  48. Margos G, Hepner S, Mang C, Marosevic D, Reynolds SE et al. Lost in plasmids: next generation sequencing and the complex genome of the tick-borne pathogen Borrelia burgdorferi . BMC Genomics 2017; 18:422 [View Article]
    [Google Scholar]
  49. Johnson RC, Hyde FW, Rumpel CM. Taxonomy of the Lyme disease spirochetes. Yale J Biol Med 1984; 57:529–537
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.003833
Loading
/content/journal/ijsem/10.1099/ijsem.0.003833
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error